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fastq-analysis-pipeline

维护者 FreedomIntelligence · 最近更新 2026年4月1日

OmicVerse provides a complete FASTQ-to-count-matrix pipeline via the `ov.alignment` module. This skill covers: - **SRA data acquisition**: `prefetch` and `fqdump` (fasterq-dump wrapper) - **Quality control**: `fastp` for adapter trimming and QC reports - **RNA-seq alignment**: `STAR` aligner with auto-index building - **Gene quantification**: `featureCount` (subread featureCounts wrapper) - **Single-cell path**: `re….

OpenClawNanoClaw分析处理复现实验fastq-analysis🧬 bioinformatics (gptomics bio-* suite)bioinformatics tools & pipelinesguide

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/fastq-analysis

维护者
FreedomIntelligence
许可
MIT
最近更新
2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

  • SRA data acquisition：prefetch 、 fqdump (fasterq-dump wrapper)。
  • Quality control：fastp ，用于 adapter trimming 、 QC reports。
  • RNA-seq alignment：STAR aligner ，支持 auto-index building。
  • Gene quantification：featureCount (subread featureCounts wrapper)。
  • Single-cell path：ref 、 count ，通过 kb-python (kallisto/bustools)。

原始文档

SKILL.md 摘录

Overview

OmicVerse provides a complete FASTQ-to-count-matrix pipeline via the ov.alignment module. This skill covers:

  • SRA data acquisition: prefetch and fqdump (fasterq-dump wrapper)
  • Quality control: fastp for adapter trimming and QC reports
  • RNA-seq alignment: STAR aligner with auto-index building
  • Gene quantification: featureCount (subread featureCounts wrapper)
  • Single-cell path: ref and count via kb-python (kallisto/bustools)
  • Parallel SRA download: parallel_fastq_dump

All functions share a common CLI infrastructure (_cli_utils.py) that handles tool resolution, auto-installation via conda/mamba, parallel execution, and streaming output.

适用场景

  • Use fastq-analysis-pipeline ，用于 single-cell 或 spatial omics analysis。
  • Apply fastq-analysis-pipeline to 聚类，integration，或 trajectory workflows。

不适用场景

  • Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

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